[gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Hi Alex,

I thought by getting the flat-bottom restraint potential on my target molecule I should be able to get the free energy of unbiased case.
Basically; P(q)=P’(q)exp(V(q)/kBT) Here P is unbiased probability, P’ is biased probability and V is added potential.
However I am not totally sure. 

You can check http://plumed.github.io/doc-v2.2/user-doc/html/belfast-4.html <http://plumed.github.io/doc-v2.2/user-doc/html/belfast-4.html>


On 17 Oct 2016, at 18:56, Alex <alexanderwien2k at gmail.com> wrote:
> 
> Hi Gozde,
> 
> I also use something similar, by an simple pull restrain(distance) to keep
> a counter ion close to the charged molecule which is under perturbation in
> FEP.
> These type of restrains are \*Lambda  *independent and if I am not wrong
> their portion in free energy change should be calculated analytically by a
> formula like something you will see in below link in its "removal of
> restrains" section;
> 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> But I have not been able to use it applicably, and I would be also
> appreciated if you could let me also know how to use if you find out either
> by this or ... .
> 
> Best regards,
> 
> Alex
> 
> On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin <gozdeeergin at gmail.com> wrote:
> 
>> Any idea?
>> Thanks.
>>> On 13 Oct 2016, at 15:42, gozde ergin <gozdeeergin at gmail.com> wrote:
>>> 
>>> Dear all,
>>> 
>>> I will use Gromacs to calculate the chemical potential difference of
>> solvation a surfactant molecule on the surface.
>>> System covers water molecules covered with surfactant molecules.
>>> I will apply flat-bottom restraint to the surfactant molecules in order
>> to stabilise them on surface. I will not let them to go inside the bulk.
>>> My question is how should I re-weight the free energy value to remove
>> the effect of flat-bottom restraint potential?
>>> 
>>> Thanks in advance.
>> 
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